* [gentoo-commits] proj/sci:master commit in: sci-biology/ssaha2-bin/
@ 2011-03-03 1:08 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2011-03-03 1:08 UTC (permalink / raw
To: gentoo-commits
commit: 77017f6cd10f5f8f6889d34d0b6c2bf2f95bbf85
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 3 01:08:39 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 3 01:08:39 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=77017f6c
sci-biology/ssaha2-bin: new package, the GRL license text extracted from the saha2-manual.pdf seems kind of ... not like a real License text
(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)
---
sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild | 1 -
1 files changed, 0 insertions(+), 1 deletions(-)
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
index 4c55b8f..eaf02be 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
@@ -41,4 +41,3 @@ src_install() {
dodoc README || die "dodoc failed"
dodoc "${DISTDIR}"/ssaha2-manual.pdf || die "Failed to install ssaha2-manual.pdf"
}
-
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ssaha2-bin/
@ 2011-03-03 1:08 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2011-03-03 1:08 UTC (permalink / raw
To: gentoo-commits
commit: b6341cabb0f9199c7207ad6aead498d64d357f95
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 3 01:01:56 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 3 01:01:56 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6341cab
sci-biology/ssaha2: new package, the GRL license text extracted from the saha2-manual.pdf seems kind of ... not like a real License text
(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)
---
sci-biology/ssaha2-bin/metadata.xml | 9 +++++
sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild | 44 ++++++++++++++++++++++++
2 files changed, 53 insertions(+), 0 deletions(-)
diff --git a/sci-biology/ssaha2-bin/metadata.xml b/sci-biology/ssaha2-bin/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/ssaha2-bin/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
new file mode 100644
index 0000000..4c55b8f
--- /dev/null
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit toolchain-funcs
+
+DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2"
+SRC_URI="x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz )
+ amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz )
+ ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz )
+ ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c
+ ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf"
+
+LICENSE="GRL"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+if use x86; then
+ S="${WORKDIR}"/ssaha2_v"${PV}"_i686
+fi
+if use amd64; then
+ S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64
+fi
+if use ia64; then
+ S="${WORKDIR}"/ssaha2_v"${PV}"_ia64
+fi
+
+src_compile() {
+ $(tc-getCC) ${CFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags"
+}
+
+src_install() {
+ dobin samflag ssaha2 ssaha2Build ssahaSNP || die "dobin failed"
+ dodoc README || die "dodoc failed"
+ dodoc "${DISTDIR}"/ssaha2-manual.pdf || die "Failed to install ssaha2-manual.pdf"
+}
+
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ssaha2-bin/
@ 2011-06-25 17:21 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2011-06-25 17:21 UTC (permalink / raw
To: gentoo-commits
commit: b6d26e31654a901b96d326eaef0e3c991fd9aad8
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 13:03:01 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 25 13:03:01 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6d26e31
Cleaned ebuild and fixed LICENSE
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/ssaha2-bin/ChangeLog | 7 ++++
sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild | 41 +++++++++--------------
2 files changed, 23 insertions(+), 25 deletions(-)
diff --git a/sci-biology/ssaha2-bin/ChangeLog b/sci-biology/ssaha2-bin/ChangeLog
new file mode 100644
index 0000000..914725e
--- /dev/null
+++ b/sci-biology/ssaha2-bin/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/ssaha2-bin
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ssaha2-bin-2.5.3.ebuild:
+ Cleaned ebuild and fixed LICENSE
+
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
index eaf02be..34b63dd 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
@@ -1,43 +1,34 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=4
inherit toolchain-funcs
DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2"
-SRC_URI="x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz )
- amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz )
- ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz )
- ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c
- ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf"
-
-LICENSE="GRL"
+SRC_URI="
+ x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz )
+ amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz )
+ ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz )
+ ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c
+ ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf"
+
+LICENSE="as-is"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-if use x86; then
- S="${WORKDIR}"/ssaha2_v"${PV}"_i686
-fi
-if use amd64; then
- S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64
-fi
-if use ia64; then
- S="${WORKDIR}"/ssaha2_v"${PV}"_ia64
-fi
+use x86 && S="${WORKDIR}"/ssaha2_v"${PV}"_i686
+use amd64 && S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64
+use ia64 && S="${WORKDIR}"/ssaha2_v"${PV}"_ia64
src_compile() {
- $(tc-getCC) ${CFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags"
+ $(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags"
}
src_install() {
- dobin samflag ssaha2 ssaha2Build ssahaSNP || die "dobin failed"
- dodoc README || die "dodoc failed"
- dodoc "${DISTDIR}"/ssaha2-manual.pdf || die "Failed to install ssaha2-manual.pdf"
+ dobin samflag ssaha2 ssaha2Build ssahaSNP
+ dodoc README "${DISTDIR}"/ssaha2-manual.pdf
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ssaha2-bin/
@ 2021-02-05 11:51 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-05 11:51 UTC (permalink / raw
To: gentoo-commits
commit: 5bb0dbb05332351ccc812a700b83ef9da63ca9dd
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Feb 5 11:29:35 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Feb 5 11:29:35 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5bb0dbb0
sci-biology/ssaha2-bin: update homepage
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
index 34f157b23..70f5a00a1 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -9,7 +9,7 @@ MY_PN="${PN%-bin}"
MY_P="${MY_PN}_v${PV}"
DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2"
+HOMEPAGE="https://www.sanger.ac.uk/tool/ssaha2-0/"
SRC_URI="
x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_i686.tgz )
amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_x86_64.tgz )
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ssaha2-bin/
@ 2021-03-06 14:55 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 14:55 UTC (permalink / raw
To: gentoo-commits
commit: ef213e7064ef4c0edb972d7a3caec58e050d1f33
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 14:50:45 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 14:50:45 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ef213e70
sci-biology/ssaha2-bin: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
index 70f5a00a1..3122e2188 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit toolchain-funcs
@@ -19,7 +19,6 @@ SRC_URI="
LICENSE="all-rights-reserved"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
QA_PREBUILT="/opt/.*"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ssaha2-bin/
@ 2022-01-25 19:15 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 19:15 UTC (permalink / raw
To: gentoo-commits
commit: 55eaf4a3f112c53b328f1d861aa2aec4f211e802
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 16:18:58 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 16:18:58 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=55eaf4a3
sci-biology/ssaha2-bin: fix WORKDIR PMS violation
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
...{ssaha2-bin-2.5.5.ebuild => ssaha2-bin-2.5.5-r1.ebuild} | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
similarity index 86%
rename from sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
rename to sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
index 3122e2188..2c0d5f63d 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
@@ -20,9 +20,10 @@ LICENSE="all-rights-reserved"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-QA_PREBUILT="/opt/.*"
+QA_PREBUILT="*"
-pkg_setup() {
+src_unpack() {
+ default
use x86 && export S="${WORKDIR}"/${MY_P}_i686
use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64
}
@@ -31,8 +32,7 @@ src_compile() {
}
src_install() {
- dobin samflag
- exeinto /opt/bin
- doexe ssaha2 ssaha2Build ssahaSNP
+ dobin samflag ssaha2 ssaha2Build ssahaSNP
dodoc README "${DISTDIR}"/ssaha2-manual.pdf
+ einstalldocs
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
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